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An official report has highlighted concerns New Zealand's charitable sector may be misused to evade tax or launder money after three local charities holding $140 million run by Swiss lawyers refused to disclose to investigators who they acted for.

An Internal Affairs Charities Service investigation dubbed "Operation Timepiece" into the New Zealand-registered Mulligan, Shepherd and Birdy Charitable Trusts found while some donations were made locally to Starship and Plunket, the vast majority of its distributions - almost $5m since 2012 - were directed offshore to a related Swiss entity called Fondation Eagle.

Officials concluded the complex structure - involving multiple layers of entities from New Zealand, Switzerland, Panama and the Isle of Man, $140m in foreign currencies and a stock portfolio managed at Swiss banks - was likely designed to avoid the scrutiny of the United States' Inland Revenue Service.

The report, prepared in December last year by Internal Affairs, said the investigation revealed a "high risk to the international reputation of New Zealand's tax and charitable systems", but was unable to be progressed due to "jurisdictional issues".

Yves Bonnard, a Geneva-based trust lawyer with a central role in the charities, said while aware the Charities Service had been asking questions he was only made aware of the report after being forwarded it by the Weekend Herald.

"I thought maybe they understood and were pleased with our answers. Until we saw this report, which is horrible," he said.

Bonnard said he would co-operate with any further investigations and said his operation was entirely above-board, and he rejected the reports' findings. "We have absolutely nothing to hide, except the identity of the donor," he said.

The investigation report was obtained under the Official Information Act by the Herald as part of its Opening the Charity Box series looking at the health of New Zealand's $53 billion charitable sector.

Spokespeople for Plunket and Starship said they had accepted donations, totalling $675,000 since 2012, from the registered charities on good faith.

In the weeks before the Charities Service finalised its report on December 19, all three charities were voluntarily deregistered. Bonnard said "the timing was simply coincidental".

The New Zealand connection is the Queen St-based Asiaciti Trust, which provided an office address and directors - Lauren Willis, Megan Wu and Kevin Taylor - for the three trustee companies governing the charities.

Willis, the managing director of Asiaciti Trust New Zealand, said repeatedly in response to questions this week: "I can't really comment, because this is bound by client confidentiality."

University of Auckland Professor Craig Elliffe said the structuring outlined in Operation Timepiece - using multiple exotic jurisdictions and multiple layers - was "very odd".

"I think this has historically been commonplace, but not with all these charitable overlays. This is probably a classic example of why we had the Shewan report," he said.

Labour Party New Lynn candidate and former Massey University tax lecturer Deborah Russell said the arrangement was "very clever".

"The sort of very clever that should ring alarm bells," she said.

One senior lawyer involved in the foreign trusts industry, speaking on condition of anonymity, said expenses incurred by the charities looked at in Operation Timepiece seemed high.

In the past three years for which accounts for the charities are available, a total of $4.1m was paid in legal, structure and trustee fees, while $5.7m was distributed - the majority to Fondation Eagle, controlled by many of the same lawyers.

"This seems to be more of a charity for lawyers," the senior lawyer said.

Bonnard did not dispute the figures but said they were in line with industry practice. Expenses were inflated partly because they included the overheads of Fondation Eagle, which operated as a Swiss-New Zealand hybrid.

"I don't disagree with you, we are well-paid and we consider it fair remuneration," he said.

Bonnard said Fondation Eagle was established in Switzerland in 2004, complied with all local regulations including filing audited accounts with Swiss authorities, and was in recent years making "one to two million" in annual donations.

He said it was structured to hold its wealth in New Zealand in order allow the charity to more easily contribute to smaller projects in the developing world.